Package: arrayQualityMetrics 3.68.0

Hugo Gruson

arrayQualityMetrics: Quality metrics report for microarray data sets

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

Authors:Audrey Kauffmann [aut], Wolfgang Huber [aut], Hugo Gruson [cre]

arrayQualityMetrics_3.68.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
arrayQualityMetrics/json (API)
NEWS

# Install 'arrayQualityMetrics' in R:
install.packages('arrayQualityMetrics', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/huber-group-embl/arrayqualitymetrics/issues

On BioConductor:arrayQualityMetrics-3.69.1(bioc 3.24)arrayQualityMetrics-3.68.0(bioc 3.23)

microarrayqualitycontrolonechanneltwochannelreportwritingbioconductor

8.04 score 1 stars 301 scripts 1.0k downloads 190 mentions 19 exports 115 dependencies

Last updated from:846e042bc4 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR220
linux-devel-x86_64NOTE262
source / vignettesOK522
linux-release-x86_64NOTE285
macos-release-arm64NOTE237
macos-oldrel-arm64NOTE224
windows-develNOTE214
windows-releaseNOTE161
windows-oldrelNOTE233
wasm-releaseOK168

Exports:addXYfromGALaqm.boxplotaqm.densityaqm.heatmapaqm.maplotaqm.meansdaqm.nuseaqm.pcaaqm.pmmmaqm.probesmapaqm.rleaqm.rnadegaqm.spatialaqm.writereportarrayQualityMetricsboxplotOutliersoutliersprepaffyprepdata

Dependencies:affyaffyioaffyPLMannotateAnnotationDbiaskpassbackportsbase64encbeadarrayBeadDataPackRBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobbslibcachemcheckmatecliclustercolorspacecpp11crayoncurldata.tableDBIdeldirdigestevaluatefarverfastmapfontawesomeforeignFormulafsgcrmagenefiltergenericsGenomicRangesggplot2gluegridExtragridSVGgtablehexbinhighrHmischtmlTablehtmltoolshtmlwidgetshttrhwriterinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglatticelatticeExtralifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigplyrpngpreprocessCoreR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownrpartRSQLiterstudioapiS4VectorsS7sassscalesSeqinfosetRNGstatmodstringistringrsurvivalsvglitesyssystemfontstextshapingtinytexvctrsviridisLitevsnwithrxfunXMLxtableXVectoryaml

Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output

Audrey Kauffmann, Wolfgang Huber

Rendered fromaqm.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2026-03-25
Started: 2026-03-25

Introduction: microarray quality assessment with arrayQualityMetrics

Audrey Kauffmann, Wolfgang Huber

Rendered fromarrayQualityMetrics.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2026-03-25
Started: 2026-03-25

Readme and manuals

Help Manual

Help pageTopics
Computing the coordinates of the spots on a slideaddXYfromGAL addXYfromGAL-methods
Write a quality reportaqm.writereport
Class to contain all the information to render a quality report module.aqmReportModule aqmReportModule-class class:aqmReportModule
Quality metrics for microarray experimentsarrayQualityMetrics
Functions for computing quality report modules.aqm.boxplot aqm.density aqm.heatmap aqm.maplot aqm.meansd aqm.nuse aqm.pca aqm.pmmm aqm.probesmap aqm.rle aqm.rnadeg aqm.spatial
Represents the results from applying an outlier detection criterion to the arrays.class:outlierDetection outlierDetection outlierDetection-class
Helper functions for outlier detection and reporting in arrayQualityMetricsboxplotOutliers outliers
Compute useful summary statistics from a data object.prepaffy prepdata